@genome-spy/core 0.36.0 → 0.37.0

package/dist/src/genome/scaleLocus.js

@@ -0,0 +1,101 @@
+import { tickStep } from "d3-array";
+import { format as d3format } from "d3-format";
+import scaleIndex from "./scaleIndex.js";
+
+export default function scaleLocus() {
+    /** @type {import("./scaleLocus").ScaleLocus} */
+    const scale = /** @type {any} */ (scaleIndex().numberingOffset(1));
+
+    /** @type {import("./genome").default} */
+    let genome;
+
+    // @ts-expect-error
+    scale.genome = function (_) {
+        if (arguments.length) {
+            genome = _;
+            return scale;
+        } else {
+            return genome;
+        }
+    };
+
+    scale.ticks = (count) => {
+        if (!genome) {
+            return [];
+        }
+
+        const domain = scale.domain();
+        const numberingOffset = scale.numberingOffset();
+
+        const [minChrom, maxChrom] = [
+            Math.max(domain[0], 0),
+            Math.min(domain[1], genome.totalSize - 1),
+        ].map((x) => genome.toChromosome(x));
+
+        const step = Math.max(1, tickStep(domain[0], domain[1], count));
+
+        const ticks = [];
+
+        for (let i = minChrom.index; i <= maxChrom.index; i++) {
+            const chrom = genome.chromosomes[i];
+
+            const from = Math.max(
+                chrom.continuousStart + step,
+                domain[0] - ((domain[0] - chrom.continuousStart) % step)
+            );
+            const to = Math.min(chrom.continuousEnd - step / 4, domain[1] + 1);
+            for (let pos = from; pos <= to; pos += step) {
+                const tick = pos - numberingOffset;
+                if (tick >= domain[0] && tick < domain[1]) {
+                    ticks.push(tick);
+                }
+            }
+        }
+
+        return ticks;
+    };
+
+    scale.tickFormat = (count, specifier) => {
+        if (!genome) {
+            return;
+        }
+
+        if (specifier) {
+            throw new Error(
+                "Locus scale's tickFormat does not support a specifier!"
+            );
+        }
+
+        const domain = scale.domain();
+        const domainSpan = domain[1] - domain[0];
+        const numberingOffset = scale.numberingOffset();
+
+        const step = tickStep(
+            domain[0],
+            domain[1],
+            Math.min(count, Math.ceil(domainSpan))
+        );
+        // Use higher display precision for smaller spans
+        // TODO: max absolute value should be taken into account too. 2.00M vs 200M
+        const numberFormat = step < 1e6 ? d3format(",") : d3format(".3s");
+
+        /** @type {function(number):number} */
+        const fixer = (x) => x - genome.toChromosome(x).continuousStart;
+
+        return /** @param {number} x */ (x) =>
+            numberFormat(fixer(x) + numberingOffset);
+    };
+
+    const originalCopy = scale.copy;
+
+    scale.copy = () => originalCopy().genome(genome);
+
+    return scale;
+}
+
+/**
+ * @type {import("./scaleLocus").isScaleLocus}
+ */
+export function isScaleLocus(scale) {
+    return scale.type == "locus";
+}

package/dist/src/genome/scaleLocus.test.js

@@ -0,0 +1,4 @@
+import { test } from "vitest";
+import scaleLocus from "./scaleLocus";
+
+test.todo("Write some tests!");

package/dist/src/genomeSpy.d.ts

@@ -0,0 +1,141 @@
+export default class GenomeSpy {
+    /**
+     * @typedef {import("./view/view").default} View
+     * @typedef {import("./spec/view").ViewSpec} ViewSpec
+     * @typedef {import("./spec/root").RootSpec} RootSpec
+     * @typedef {import("./spec/root").RootConfig} RootConfig
+     */
+    /**
+     *
+     * @param {HTMLElement} container
+     * @param {RootSpec} spec
+     * @param {import("./types/embedApi").EmbedOptions} [options]
+     */
+    constructor(container: HTMLElement, spec: import("./spec/root").RootSpec, options?: import("./types/embedApi").EmbedOptions);
+    container: HTMLElement;
+    /** Root level configuration object */
+    spec: import("./spec/root").RootSpec;
+    accessorFactory: AccessorFactory;
+    viewFactory: ViewFactory;
+    /** @type {(function(string):object[])[]} */
+    namedDataProviders: ((arg0: string) => object[])[];
+    animator: Animator;
+    /** @type {GenomeStore} */
+    genomeStore: GenomeStore;
+    /**
+     * View visibility is checked using a predicate that can be overridden
+     * for more dynamic visibility management.
+     *
+     * @type {(view: View) => boolean}
+     */
+    viewVisibilityPredicate: (view: import("./view/view").default) => boolean;
+    /** @type {BufferedViewRenderingContext} */
+    _renderingContext: BufferedViewRenderingContext;
+    /** @type {BufferedViewRenderingContext} */
+    _pickingContext: BufferedViewRenderingContext;
+    /** Does picking buffer need to be rendered again */
+    _dirtyPickingBuffer: boolean;
+    /**
+     * Currently hovered mark and datum
+     * @type {{ mark: import("./marks/mark").default, datum: import("./data/flowNode").Datum, uniqueId: number }}
+     */
+    _currentHover: {
+        mark: import("./marks/mark").default;
+        datum: import("./data/flowNode").Datum;
+        uniqueId: number;
+    };
+    _wheelInertia: Inertia;
+    /**
+     * Keeping track so that these can be cleaned up upon finalization.
+     * @type {Map<string, (function(KeyboardEvent):void)[]>}
+     */
+    _keyboardListeners: Map<string, ((arg0: KeyboardEvent) => void)[]>;
+    /**
+     * Listers for exposed high-level events such as click on a mark instance.
+     * These should probably be in the View class and support bubbling through
+     * the hierarchy.
+     *
+     * @type {Map<string, Set<(event: any) => void>>}
+     */
+    _eventListeners: Map<string, Set<(event: any) => void>>;
+    /**
+     *
+     * @type {Map<string, Set<(event: any) => void>>}
+     */
+    _extraBroadcastListeners: Map<string, Set<(event: any) => void>>;
+    /** @type {Record<string, import("./tooltip/tooltipHandler").TooltipHandler>}> */
+    tooltipHandlers: Record<string, import("./tooltip/tooltipHandler").TooltipHandler>;
+    /** @type {View} */
+    viewRoot: import("./view/view").default;
+    /**
+     *
+     * @param {(name: string) => any[]} provider
+     */
+    registerNamedDataProvider(provider: (name: string) => any[]): void;
+    /**
+     * @param {string} name
+     */
+    getNamedDataFromProvider(name: string): object[];
+    /**
+     *
+     * @param {string} name
+     * @param {any[]} data
+     */
+    updateNamedData(name: string, data: any[]): void;
+    /**
+     * Broadcast a message to all views
+     
+     * @param {BroadcastEventType} type
+     * @param {any} [payload]
+     */
+    broadcast(type: BroadcastEventType, payload?: any): void;
+    _prepareContainer(): void;
+    _glHelper: WebGLHelper;
+    loadingMessageElement: HTMLDivElement;
+    tooltip: Tooltip;
+    /**
+     * Unregisters all listeners, removes all created dom elements, removes all css classes from the container
+     */
+    destroy(): void;
+    _prepareViewsAndData(): Promise<void>;
+    /**
+     * TODO: Come up with a sensible name. And maybe this should be called at the end of the constructor.
+     * @returns {Promise<boolean>} true if the launch was successful
+     */
+    launch(): Promise<boolean>;
+    registerMouseEvents(): void;
+    _tooltipUpdateRequested: boolean;
+    /**
+     * @param {number} x
+     * @param {number} y
+     */
+    _handlePicking(x: number, y: number): void;
+    /**
+     * This method should be called in a mouseMove handler. If not called, the
+     * tooltip will be hidden.
+     *
+     * @param {T} datum
+     * @param {function(T):Promise<string | HTMLElement | import("lit").TemplateResult>} [converter]
+     * @template T
+     */
+    updateTooltip<T>(datum: T, converter?: (arg0: T) => Promise<string | HTMLElement | import("lit").TemplateResult>): void;
+    computeLayout(): void;
+    renderAll(): void;
+    renderPickingFramebuffer(): void;
+    getSearchableViews(): UnitView[];
+    getNamedScaleResolutions(): Map<string, import("./view/scaleResolution").default>;
+}
+/**
+ * Events that are broadcasted to all views.
+ */
+export type BroadcastEventType = "dataFlowBuilt" | "dataLoaded" | "layout" | "layoutComputed";
+import AccessorFactory from "./encoder/accessor";
+import { ViewFactory } from "./view/viewFactory";
+import Animator from "./utils/animator";
+import GenomeStore from "./genome/genomeStore";
+import BufferedViewRenderingContext from "./view/renderingContext/bufferedViewRenderingContext";
+import Inertia from "./utils/inertia";
+import WebGLHelper from "./gl/webGLHelper";
+import Tooltip from "./utils/ui/tooltip";
+import UnitView from "./view/unitView";
+//# sourceMappingURL=genomeSpy.d.ts.map

package/dist/src/genomeSpy.d.ts.map

@@ -0,0 +1 @@
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